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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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RiboTaper Resource Report Resource Website 1+ mentions |
RiboTaper (RRID:SCR_018880) | data analysis software, data processing software, software application, software resource | Software tool as analysis pipeline for ribosome profiling experiments, which exploits triplet periodicity of ribosomal footprints to call translated regions. Statistical approach that identifies translated regions on basis of characteristic three nucleotide periodicity of Ribo-seq data. | Ribo-seq data, analysis, ribosome profiling experiment, triplet periodicity, ribosomal footprint, translated region, three nucleotide periodicity, data, ribosome profiling, bio.tools |
is listed by: bio.tools is listed by: Debian |
Berlin Institute for Medical Systems Biology ; NIGMS R01 GM104962 |
PMID:26657557 | Free, Freely available | biotools:ribotaper | https://bioconda.github.io/recipes/ribotaper/README.html, https://bio.tools/ribotaper | SCR_018880 | SciCrunch Registry | 2026-10-24 12:48:04 | 8 | ||||||
|
Vmatch Resource Report Resource Website 50+ mentions |
Vmatch (RRID:SCR_018968) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool for efficiently solving large scale sequence matching tasks. | Sequence analysis, large scale, sequence matching, sequence, matching, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools is listed by: SoftCite has parent organization: University of Hamburg; Hamburg; Germany |
Free, Available for download, Freely available | OMICS_19963, biotools:vmatch | https://bio.tools/vmatch, https://sources.debian.org/src/vmatch/ | SCR_018968 | SciCrunch Registry | 2026-10-24 12:48:05 | 56 | ||||||||
|
LTR_FINDER_parallel Resource Report Resource Website 10+ mentions |
LTR_FINDER_parallel (RRID:SCR_018969) | data analysis software, data processing software, software application, software resource | Software tool for parallelization of LTR_FINDER enabling rapid identification of long terminal repeat retrotransposons. | Parallelization, rapid identification, retrotransposons identification, repetitive sequences, large genomes, long terminal repeat, retrotrnsposon, parallel operation, bio.tools |
is listed by: bio.tools is listed by: Debian |
Agriculture and AgBioResearch at Michigan State University ; NSF IOS 1740874; United States Department of Agriculture National Institute of Food |
PMID:31857828 | Free, Available for download, Freely available | biotools:LTR_FINDER_parallel | https://bio.tools/LTR_FINDER_parallel | SCR_018969 | SciCrunch Registry | 2026-10-24 12:48:05 | 15 | ||||||
|
metaXplor Resource Report Resource Website 1+ mentions |
metaXplor (RRID:SCR_019025) | data or information resource, software resource, web application | Web interfaced application to store, share, explore and manipulate metagenomic data. Interactive viral and microbial metagenomic data manager. Stores large volumes of user defined sample, sequence and assignment information while providing filtering web interface. Offers means to share datasets with collaborators, BLAST external sequences against them, and confirm assignments by running phylogenetic placement. Available as set of Docker containers that make it simple to deploy on various infrastructures. | Data storage, metagenomics, data filtering, data sharing, data exploration, metagenomic data, viral data, microbial data, data manager, datasets sharing, bio.tools |
is listed by: bio.tools is listed by: Debian |
Restricted | biotools:metaxplor | https://metaxplor.cirad.fr/metaXplor/, https://bio.tools/metaxplor | SCR_019025 | SciCrunch Registry | 2026-10-24 12:48:06 | 1 | ||||||||
|
GigaSOM.jl Resource Report Resource Website 1+ mentions |
GigaSOM.jl (RRID:SCR_019020) | data processing software, data visualization software, software application, software resource | Software tool for huge scale, high performance flow cytometry data clustering and visualization in Julia. High performance clustering and visualization of huge cytometry datasets. | Flow cytometry data, flow cytometry data clustering, data clustering, data visualization, Julia, datasets, bio.tools |
is listed by: Debian is listed by: bio.tools |
DOI:10.1101/2020.08.03.234187 | Free, Available for download, Freely available | biotools:GigaSOM.jl | https://bio.tools/GigaSOM.jl | SCR_019020 | SciCrunch Registry | 2026-10-24 12:48:06 | 2 | |||||||
|
TRAL Resource Report Resource Website 1+ mentions |
TRAL (RRID:SCR_018979) | TRAL | algorithm resource, data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to make annotation of tandem repeats in amino acid and nucleic data simple. Includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs. Used for statistical significance analysis of putative tandem repeats, and filtering of redundant predictions. | Annotation, tandem repeats annotation, amino acid repeats, nucleic data, statistical analysis, redundant predictions filtering, redundant annotation clustering, overlapping annotations clustering, false positive annotation filtering, bio.tools |
is listed by: bio.tools is listed by: Debian |
Swiss State Secretariat for Education ; Research ; and Innovation |
DOI:10.1093/bioinformatics/btv306 | Free, Freely available | biotools:tral | https://bio.tools/tral | SCR_018979 | SciCrunch Registry | Tandem Repeat Annotation Library | 2026-10-24 12:48:05 | 1 | ||||
|
VICMpred Resource Report Resource Website 1+ mentions |
VICMpred (RRID:SCR_019039) | data access protocol, software resource, web service | Software tool as SVM based method for prediction of functional proteins of gram negative bacteria using amino acid patterns and composition. Webserver for functional classification of proteins of bacteria into virulence factors, information molecule, cellular process and metabolism molecule. | Bacterial protein, protein functional classification, virulence factor, metabolism molecule, information molecule, cellular process, gram negative bacteria, functional proteins prediction, amino acid patterns, aminoacid composition, dipeptide composition, bacterial protein sequences., bio.tools |
is listed by: Debian is listed by: bio.tools |
Council of Scientific and Industrial Research and Department of Biotechnology ; Government of India |
PMID:16689701 | Free, Freely available | biotools:vicmpred | https://bio.tools/vicmpred | SCR_019039 | SciCrunch Registry | Cellular process and Metabolism molecule in the bacterial proteins., Information molecule, Prediction of Virulence factors | 2026-10-24 12:48:06 | 3 | |||||
|
Annotree Resource Report Resource Website 10+ mentions |
Annotree (RRID:SCR_018980) | data access protocol, data or information resource, software resource, web service | Web tool for visualization of genome annotations across large phylogenetic trees.Used for visualization and exploration of functionally annotated microbial tree of life. Integrates taxonomic, phylogenetic and functional annotation data from bacterial and archaeal genomes. | Genome annotation, genome visualization, phylogenetic tree, functionally annotated tree, microbial tree of life, taxonomic data, phylogenetic data, functionally annotated data, bacterial genome, archaeal genome, genome distribution, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
Australian Research Council Laureate Fellowship ; Natural Sciences and Engineering Research Council of Canada ; NSERC Discovery Grant ; Ontario Early Researcher award ; Tier II Canada Research Chair |
PMID:31081040 | Free, Freely available | biotools:Annotree | https://bio.tools/AnnoTree | SCR_018980 | SciCrunch Registry | AnnoTree 1.2 | 2026-10-24 12:48:05 | 25 | |||||
|
Pyntacle Resource Report Resource Website 1+ mentions |
Pyntacle (RRID:SCR_019030) | data analysis software, data processing software, network analysis software, software application, software resource | Software Python package and command line tool for graphs analysis. Used to search for important components of graphs. Implements and provides ancillary methods for community finding, set operations between graphs, and quick data type conversion tools. | Graph analysis, topology, group centrality, systems biology, parallel computing, data conversion tool, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:pyntacle | https://bio.tools/pyntacle | SCR_019030 | SciCrunch Registry | 2026-10-24 12:48:06 | 1 | ||||||||
|
BRAKER Resource Report Resource Website 500+ mentions |
BRAKER (RRID:SCR_018964) | simulation software, software application, software resource | Software tool as pipeline for accurate and automated gene prediction in novel eukaryotic genomes. Automated gene prediction training and gene prediction pipeline.BRAKER1 is eukaryotic genome annotation pipeline. BRAKER2 is extension of BRAKER1 which allows for fully automated training of gene prediction tools GeneMark EX R14, R15, R17, F1 and AUGUSTUS from RNA Seq and/or protein homology information, and that integrates extrinsic evidence from RNA-Seq and protein homology information into prediction. | Automated gene prediction, novel eukaryotic genomes, gene prediction training, gene prediction pipeline, protein coding gene structure, gene structure prediction, eukaryotic genome, RNA-Seq, protein homology |
uses: Augustus is listed by: Debian is listed by: OMICtools |
German Research Foundation ; NHGRI HG000783 |
PMID:31020555 DOI:10.1101/2020.08.10.245134 |
Free, Available for download, Freely available | OMICS_10582 | https://sources.debian.org/src/braker/ | SCR_018964 | SciCrunch Registry | BRAKER2, BRAKER1 | 2026-10-24 12:48:05 | 531 | |||||
|
IMGT/StatClonotype Resource Report Resource Website 1+ mentions |
IMGT/StatClonotype (RRID:SCR_018963) | data analysis software, data processing software, software application, software resource | Software tool to evaluate and visualize statistical significance of pairwise comparisons of IMGT clonotype (AA) diversity or expression, per variable,diversity, and joining gene of given IG or TR group, from NGS IMGT/HighV-QUEST statistical output. Antibody clonotype analysis based on NGS sequences. | T cell receptor, antibody, immunoglobulin, immunoinformatics, next generation sequencing, statistical significance, clonotype diversity, clonotype expression, pairwise comparison, gene, NGS, analysis, antybody clonotype, bio.tools |
is listed by: bio.tools is listed by: Debian |
PMID:27667992 | Free, Available for download, Freely available | biotools:IMGt_StatClonotype | https://bio.tools/IMGT_StatClonotype | SCR_018963 | SciCrunch Registry | IMGTStatClonotype, ImMunoGeneTics/StatClonotype | 2026-10-24 12:48:05 | 4 | ||||||
|
ClinTrajAn Resource Report Resource Website 1+ mentions |
ClinTrajAn (RRID:SCR_019018) | data analysis software, data processing software, data visualization software, software application, software resource | Software Python package for analysis of trajectories in clinical datasets. | Trajectories analysis, clinical datasets, analysis, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:clintrajan | https://bio.tools/clintrajan | SCR_019018 | SciCrunch Registry | 2026-10-24 12:48:05 | 1 | ||||||||
|
Seqtk Resource Report Resource Website 1000+ mentions |
Seqtk (RRID:SCR_018927) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software fast and lightweight tool for processing sequences in FASTA or FASTQ format. | Sequence processing, FASTA format, FASTQ format, data processing, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_09736, biotools:seqtk | https://bio.tools/seqtk, https://sources.debian.org/src/seqtk/ | SCR_018927 | SciCrunch Registry | SEQTK | 2026-10-24 12:48:04 | 1039 | |||||||
|
D-EE Resource Report Resource Website 1+ mentions |
D-EE (RRID:SCR_019058) | data analysis software, data processing software, data visualization software, software application, software resource | Software tool for distributed dimensionality reduction and visualization. Distributed software for visualizing intrinsic structure of large scale single cell data written in C language. Its distributed storage and distributed computation technique allows efficiently analyze large scale single cell data at cost of constant time speedup. | Distributed dimensionality reduction, dimensionality reduction, distributed storage, distributed computation, large scale data, single cell data, data, , bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:d-ee | https://bio.tools/d-ee | SCR_019058 | SciCrunch Registry | 2026-10-24 12:48:06 | 1 | ||||||||
|
ReactomePA Resource Report Resource Website 50+ mentions |
ReactomePA (RRID:SCR_019316) | data analysis software, data processing software, data visualization software, software application, software resource | Software R package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization. | pathway analysis, REACTOME pathway, REACTOME database, enrichment analysis, gene set enrichment analysis, bio.tools |
is listed by: Bioconductor is listed by: bio.tools is listed by: Debian |
PMID:26661513 | Free, Available for download, Freely available | biotools:reactomepa | https://bio.tools/reactomepa | SCR_019316 | SciCrunch Registry | Reactome Pathway Analysis | 2026-10-24 12:48:09 | 86 | ||||||
|
GEDIT Resource Report Resource Website 10+ mentions |
GEDIT (RRID:SCR_019277) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Software tool for accurate cell type quantification from gene expression data. Uses gene expression data to estimate cell type abundances. Allows user to supply custom reference matrices. | bio.tools |
is listed by: bio.tools is listed by: Debian |
DOI:10.1101/728493 | Free, Freely available | biotools:gedit | http://webtools.mcdb.ucla.edu/, https://bio.tools/gedit | SCR_019277 | SciCrunch Registry | Gene Expression Deconvolution Interactive Tool | 2026-10-24 12:48:09 | 12 | ||||||
|
Gmove Resource Report Resource Website 1+ mentions |
Gmove (RRID:SCR_019132) | simulation software, software application, software resource | Software tool for genome annotation. Eukaryotic gene prediction tool focused on evidence supported by expressed sequences like transcripts and conserved proteins alignments. Can be used to reannotate genomes, to do comparative gene prediction and improve existing genome annotation. Can predict gene models with canonical and non-canonical splice sites. | Expressed sequences, RNAseq, conserved proteins, conserved proteins alignment, genome annotation, Eukaryotic gene prediction, gene prediction, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:gmove | https://github.com/institut-de-genomique/gmove, https://bio.tools/gmove | SCR_019132 | SciCrunch Registry | Gene MOdeling using Various Evidence | 2026-10-24 12:48:07 | 3 | |||||||
|
MetaBAT Resource Report Resource Website 500+ mentions |
MetaBAT (RRID:SCR_019134) | data analysis software, data processing software, software application, software resource | Software statistical framework for reconstructing genomes from metagenome data. Open source software tool for accurately reconstructing single genomes from complex microbial communities. | Genome bin, metagenome datasets, reconstructing single genomes, microbial communities, metagenome data | is listed by: Debian | PMID:26336640 | Free, Available for download, Freely available | https://bitbucket.org/berkeleylab/metabat/wiki/CAMI, https://sources.debian.org/src/metabat/ | SCR_019134 | SciCrunch Registry | MetaBAT2 | 2026-10-24 12:48:07 | 761 | |||||||
|
SoupX Resource Report Resource Website 50+ mentions |
SoupX (RRID:SCR_019193) | data analysis software, data processing software, software application, software resource, software toolkit | Software R package for estimation and removal of cell free mRNA contamination in droplet based single cell RNA-seq data. | Estimation, removal, cell free mRNA contamination, droplet based, single cell RNA-seq data, RNA-seq data, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:soupx | https://bio.tools/soupx | SCR_019193 | SciCrunch Registry | 2026-10-24 12:48:08 | 87 | ||||||||
|
tradeSeq Resource Report Resource Website 10+ mentions |
tradeSeq (RRID:SCR_019238) | data analysis software, data processing software, software application, software resource | Software tool as suite of tests for identifying dynamic temporal gene regulation using single cell RNA-seq data.Trajectory based differential expression analysis for sequencing data. | Dynamic temporal gene regulation, gene regulation identifying, gene regulation, single cell RNA-seq data, differential expression analysis, sequencing data, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download, Freely available | biotools:tradeseq | https://bioconductor.org/packages/tradeSeq/, https://bio.tools/tradeseq | SCR_019238 | SciCrunch Registry | TRAjectory-based Differential Expression analysis for SEQuencing data | 2026-10-24 12:48:09 | 47 |
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